rs6992620

Variant names:

• chr8-80723736-C-A
• rs6992620
• NM_001033723.3:c.222-30629G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-80723736-C-A
• chr8-80723736-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001033723.3(ZNF704):​c.222-30629G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZNF704 NM_001033723.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

Genes affected

ZNF704 (HGNC:32291): (zinc finger protein 704) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF704	NM_001033723.3	c.222-30629G>T		intron_variant	Intron 2 of 8	ENST00000327835.7	NP_001028895.1
ZNF704	NM_001367783.1	c.744-30629G>T		intron_variant	Intron 2 of 8		NP_001354712.1
ZNF704	XM_017013725.2	c.246-30629G>T		intron_variant	Intron 2 of 8		XP_016869214.1
ZNF704	XR_928797.3	n.1168-30629G>T		intron_variant	Intron 2 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF704	ENST00000327835.7	c.222-30629G>T		intron_variant	Intron 2 of 8	1	NM_001033723.3	ENSP00000331462.3
ZNF704	ENST00000519936.2	c.744-30629G>T		intron_variant	Intron 2 of 8	5		ENSP00000427715.2
ZNF704	ENST00000520336.1	n.149-29428G>T		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.1
DANN	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6992620; hg19: chr8-81635971;